Here is an old comparison, where APE compression ratio was better. Of course, that was still FLAC 1.1.2, I would guess 1.1.3 (or 1.1.4, which is… well… half-released, not yet on the front page and not yet binaries for all OS imho 😉 ) might already be better.

APE-Tags are something winning over FLAC though imho. Still wouldn’t want to use anything but FLAC (well, maybe ALAC to stream untranscoded to the Soundbridge 😉 ).